Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs. </jats:p

The History of Pineapple Improvement

Man has been directing the genome of pineapple for a very long time. There is some evidence to suggest the domestication process started around 6000 years ago. The methods for breeding have of course changed considerably from the earliest times of pineapple domestication, but we still are seeking much the same goals. So much so that one of the cultivars to emerge from that early domestication, ‘Smooth Cayenne’, is still the predominant processing pineapple worldwide. The most modern pineapple genotypes today are only about eight generations removed from the early pre-Columbian village cultivars. These early pre-Columbian cultivars have in fact been the source of genetics for most pineapple breeding programs. There has been little effort to incorporate wild genetics into modern pineapple. There is in fact little need given the substantial level of heterozygosity that domestic pineapple exhibits. The high level of heterozygosity in pineapple has both been a great source of diversity for breeders and also a major bottleneck in progress. Almost all modern approaches to genome manipulation or breeding have been attempted in pineapple to overcome the problems associated with high heterozygosity including inbreeding, ploidy manipulation, mutation breeding and gene modification. Only gene editing and marker-assisted breeding have yet to make their impact in pineapple. This chapter looks at the history of pineapple breeding, the approaches used and lessons learnt in the hope we build on their successes to provide the world with more examples of the great diversity in pineapple